BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089578.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 23,515,399 number of mapped reads = 19,707,921 (83.81%) number of supplementary alignments = 772 (0%) number of secondary alignments = 0 number of mapped bases = 919,322,962 bp number of sequenced bases = 919,133,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,090,368 duplication rate = 7.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9546 >>>>>>> ACTG content number of A's = 285,830,472 bp (31.1%) number of C's = 186,564,938 bp (20.3%) number of T's = 252,551,205 bp (27.48%) number of G's = 194,186,022 bp (21.13%) number of N's = 1,155 bp (0%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 4,213,828 number of insertions = 40,283 mapped reads with insertion percentage = 0.2% number of deletions = 127,283 mapped reads with deletion percentage = 0.64% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.297X std coverageData = 1.6499X There is a 15.61% of reference with a coverageData >= 1X There is a 6.36% of reference with a coverageData >= 2X There is a 3.04% of reference with a coverageData >= 3X There is a 1.62% of reference with a coverageData >= 4X There is a 0.92% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 73924064 0.29658527510749916 2.444048810936741 chr2 243199373 78055394 0.32095228304721 2.0044467934177845 chr3 198022430 63689432 0.3216273631224503 0.9894983641469319 chr4 191154276 61652867 0.3225293636643525 1.0952612591609632 chr5 180915260 57878973 0.31992311206915325 1.0096299505658604 chr6 171115067 54732106 0.3198555624561103 1.2832325290731792 chr7 159138663 51915900 0.3262305904882461 2.30562520291761 chr8 146364022 48468853 0.3311527815216775 3.044607701764968 chr9 141213431 38405831 0.2719701003511486 1.4842548672884133 chr10 135534747 35273672 0.2602555638370727 1.5019784394031401 chr11 135006516 41440686 0.306953228835266 1.5110067396093527 chr12 133851895 43058096 0.3216846201542384 1.069938149884376 chr13 115169878 29783853 0.258608010334091 0.8946949883616107 chr14 107349540 21794226 0.2030211400999017 1.069523125013463 chr15 102531392 26590199 0.25933715012861625 0.8905040292466502 chr16 90354753 25468248 0.28186948837102127 1.0756469719944912 chr17 81195210 24530376 0.3021160484713322 1.2017344251507505 chr18 78077248 24983023 0.31997827331209217 2.4658843755327946 chr19 59128983 17558700 0.2969558938634206 2.234136455648483 chr20 63025520 19527172 0.30982960553121974 1.0765318885736117 chr21 48129895 12387608 0.25737866247163016 1.123911076523492 chr22 51304566 10333471 0.20141425618920547 0.7859987632382388 chrMT 16571 171091 10.32472391527367 9.869705582720893 chrX 155270560 55008799 0.3542770696518387 1.3858531058802952 chrY 59373566 2690322 0.0453117806668375 0.6855888289874441